Pet Battle Dungeons are very similar to normal dungeons, except that instead of fighting NPCs to continue, you must win a series of pet battles, similar to in the Celestial Tournament. In these dungeons, there are a number of stages, which may each consist of defeating a few sets of battle pets and/or a boss. The battle pets that you fight throughout the dungeon are often smaller versions of the NPCs fought in the normal version of the dungeon. In Normal mode, you can heal your battle pets between battles. However, in Challenge mode, like in the Celestial Tournament, you cannot heal your battle pets within the dungeon, though you can attempt to defeat each opponent as many times as you wish if you are unsuccessful the first time. As of Patch 7.2, there was only one pet battle dungeon, but more were later.

The Wailing Caverns dungeon consists of 12 fights, in 7 stages. After completing the dungeon, you can ask Muyani to leave the dungeon, and she will teleport you outside, where you can speak to her again to complete this quest and receive your reward, an Ultimate Battle-Training Stone. The first time you complete the dungeon, it will be in Normal mode, and you will be able to heal your pets between battles. After you complete the initial quest, however, you will receive the quest, Pet Battle Challenge: Wailing Caverns, which is to complete the dungeon again in Challenge mode, in which you cannot heal or revive your pets within the dungeon. This challenge rewards Damp Pet Supplies, and can be completed weekly.